Gene actions

Genes are one of the most important parts of the research. In ePathway, methods for an agile management of genes are provided, for actions like inserting, deleting, searching, updating and viewing. The system also implements functionality for adding primers and relevant areas to a gene, as described below.

Create a gene
When creating a gene, the following fields are required: And these fields are optional: Once all the desired information is provided, the user can click on "Create" button, to store the gene in the application's database. The site then redirects to gene list view.
 * Access code: the gene standard identificator.
 * Organism: the organism which the gene belongs to.
 * Identificator: a name used to identificate a gene. It may be standard or custom added by the researcher.
 * Complete sequence: the complete nucleotide sequence for this gene.
 * Coding Sequence (CDS): the sequence that generates this gene.

Other actions available from this page are: list genes and manage genes.

List all stored genes
When accessing the link in the actions menu for "List Genes", all the stored genes are displayed, sorted to show the most recent first.

The information displayed is: Other details
 * Identificator
 * Access code
 * Complete sequence
 * Coding sequence
 * Organism
 * A link to go to the gene's details page

When a field isn't specified, the attributed is displayed with a blank space next to it. Also, when a nucleotide sequence is too long, an horizontal scroll is added.

This page also supports pagination, so if more than 10 genes are added, they're spplited in pages and are loaded on demand.

See gene's details
In this section of the website, the details about a gene are displayed. The included fields are: For a proper display of a nucleotide sequence, in this page they are displayed with a scroll and a dynamic field, which is expanded when the cursor is placed over.
 * View_gene.pngs code
 * Identificator
 * Organism
 * Complete sequence
 * Coding Sequence

To copy the sequence, the user have to click on the sequence three times, and then press Ctrl+C.

Accesible actions from this view: list genes, create gene, update gene, delete gene, manage gene, add a primer, add a relevant area.

Also, two buttons for displaying this gene's associated primers and relevant areas are provided.

Manage and search genes
This page provides two main functionalities:

Access to view, update and delete functions, via a shortcut, using the buttons displayed next to a gene's info.

Searching functionalities: over each column's data, there's a field where a user can type expressions to be searched in the data of that column, and then press enter. In that case, the page will dynamically refresh to display the r.esults in the same table. To clear the results, the user must click out of the search area.

Advanced search functionalities: by clicking on "Advanced Search", a search form is displayed. The operators form greater than (>), less than (<), greater or equal (>=), less of equal (<=) and distinct (<>) are allowed. For example, searching with "<B" on the access code field, will return all the gene's rows with an access code starting with letters preceding "B", i.e. starting with "A".

Update a gene
The process to update a gene is pretty similar to creating one. The same fields are displayed, but in this case, the information of the gene is loaded. Also the rules about required fields, and the format for each one, are the same as the ones implemented in the "Create a gene" functionality.

After modifying the desired fields, the user must clic on save, to store the changes. Then, the site is redirected to the gene's detailed view.

Delete a gene
There are two options to delete a gene: After clicking, confirmation from the user is required.
 * Clicking in the red X on the manage view
 * Clicking on the link "Delete gene" in the actions menu for a gene

Important note: deleting a gene with associated primers or relevant areas is not allowed in this version of ePathway. In order a gene in one of this cases, the primers or relevant areas associated must be deleted first.

Adding primers and relevant areas
Details are in the corresponding sections:
 * Primer actions
 * Relevant area actions